94 5.2L Magnum running rough

My EFI training is pretty basic, but one thing I know;
OOPs my computer lost power, I'll have to reboot, be back in a sec. Ok so the programming is not letting me cut and paste so, Go to the bottom and read Note-1, then come back to the top and begin reading at Page-1

Page-1
Again, My EFI training is very basic. I'm only responding cuz this thread is on like page 15.... Ok then;
My understanding of the sequential EFI System, is like this;
The ECU, during cranking, looks to the CPS to know that the engine is cranking, and when it gets to #1; then looks to the Cam sensor to figure out on what stroke #1 is at (compression or exhaust). I believe this is called establishing synchronicity.
Once it knows that, it begins counting (18436572) from the cam-sensor signal, and never looks at the CPS again until the next restart.

It seems to me that your ECU is momentarily losing the cam signal, and forgets where it was in the counting. When that happens, I bet the ECU has no choice but to start over, and to look to the CrankPS to re-establish synchronicity.
Since the engine is spinning and has not yet stalled, it figures out where it is and starts running again. The ECU only needs a MAXIMUM of two crank revolutions to do this.
But since the engine does occasionally stall, I'm guessing there are times that it is not getting the Crank signal either!...... This would be highly unusual. More likely is that the issue is in the Power supply or the wiring, or the computer.
or the coil is going bad.

A failing coil will show up, in Closed Loop, as running rich whenever it missfires. But so will a bad injector. AND it is theO2 sensor that is fiddling with the AFR to compensate. To figure out which it is, you gotta fool the ECU into not recognizing the problem, so then, put her back into Open-Loop, which will cause the ECU to go back to it's base-programming, which is running off the CTS. This will put the O2 offline so you can actually do some diagnostics.
So now, in Open-Loop, with the CTS running the show, if nothing else, at least the O2 won't be modifying the fueling.
The base programming is really pretty good.
At this time, I would also unplug the AIS, so the Idle speed remains stable.
So now, the engine should be idling without any interference from the O2 nor any changes in rpm. Therefore, if the rpm is changing, it can only be caused by:
1) changes in ignition timing or
2) by flooding if an injector is bad. or
3) by an intermittent vacuum leak .
As to #1, the timing lite will tell the tale
As to #2, the stink out the tail pipe should clue you in
As to #3, I've never heard of that, lol.

Note-1
If the engine has an original beer-keg intake, of course the first thing to do is prove that the clean-out plate is not sucking up CC blow-by, which they are famous for doing. Proving this is pretty simple ; just flip the PCV out of the cover grommet, seal both valve covers and put a vacuum gauge on the dipstick tube, then start her up. Set up like this, the CC should immediately start building pressure, and if it does, shut it off before the pressure exceeds 3>4psi. But if the gauge reads vacuum, then the intake has got to come off and the clean-out plate resealed; then start over.